I’ve had a few issues recently with git rebase failing intermittently when there are clearly no conflicts; if you run git rebase –abort and then try the rebase again it often succeeds.

It appears that this can happen when Xcode is running in the background, as described in this discussion; the problem is that an application can be running git status in the background. My own experience supports this (closing Xcode fixes the problem), so if you’re experiencing a similar problem you may find this helpful.